Question: Erorr with runing cuffmerge
gravatar for Ath.T
4 months ago by
Ath.T20 wrote:


I am doing RNA-seq analysis, I am trying to run cuffmerge for assembled transcripts files that have been generated by cufflinks but I have got the following error:

Fatal error: Error running cuffmerge:

[Fri Jul 13 04:32:00 2018] Beginning transcriptome assembly merge

[Fri Jul 13 04:32:00 2018] Preparing output location cm_output/ [Fri Jul 13 04:32:00 2018] Converting GTF files to SAM [04:32:00] Loading reference annotation. GFF Error: duplicate/invalid 'transcript' feature ID=gene104 [FAILED] Error: could not execute gtf_to_sam

Could you please help me to solve this problem, What should I do?


rna-seq cuffmerge • 164 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson25k • written 4 months ago by Ath.T20
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This error indicates that the reference annotation GFF3 input has duplicated IDs. Most tools do not interpret duplicates well and will fail.

Two choices, with the second preferred:

  1. Find the GTF version of the annotation and use that instead. The utility gffread (converts GFF3 > GTF) will probably not help for this case (e.g. likely fail for the same duplicate reason).
  2. Switch to using newer tools such as Stringtie merge and Stringtie. The tools you are using now are much older and considered deprecated. GTF data tends to work better with these tools as well.

Tutorials that cover the latest RNA-seq methods can be found here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson25k
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